Intro to NGS processing
James A. Fellows Yates
2021-08-17
Who am I?
- Education
- B.Sc. Bioarchaeology (University of York, UK)
- M.Sc. Naturwissenschaftliches Archäologie (University of Tübingen, DE)
- Ph.D. Archaeogenetics (MPI-SHH / MPI-EVA, DE)
- Experience
- Number of genetics classes taken: 0
- Number of bioinformatics classes taken: 0
@jfy133
Today we will
- Introduce what DNA sequencing is
- Explain how Illumina NGS sequencing data is generated
- How to evaluating NGS data [Practical]
What is DNA?
Deoxyribonucleic acid (/diːˈɒksɪˌraɪboʊnjuːˌkliːɪk, -ˌkleɪ-/ (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. - Wikipedia
The rules
- Four nucleotides
- Pyrimidines:
Cytosine, Thymine
- Purines:
Guanine Adenine &
- Base pairing: one pyrimidine with one purine
C with G (think: CGI)
A to T (think: AT-AT walker)
- Complementary
C on one strand, G on the other (or v.v.)
A on one strand, T on the other (or v.v.)
The rules
- Make copy of a DNA strand with a polymerase
- Unwind the DNA
- Separate the strands
- Make new strand: find a
C, get new G (etc)
By Madprime (CC-BY-3.0 SA)
What is Sequencing?
Converting the chemical nucleotides of a DNA molecule
to
ACTG on your computer screen
What is NGS?
NGS: Next Generation Sequencing
- MASSIVELY multiplexed!
- Sequence millions and millions and millions and millions of DNA reads at once!
Not really ‘next’ anymore, consider it more ‘second’ generation (see: Nanopore)
Market leader: 